Hello Mike,
Currently, custom reports will query all projects. You could, however, create your report and in the report shortcut you can uncheck the 'Automatically filter..' option, and then specify a sort criteria such as "projectID = 3" in the Sort Criteria field. You could then create multiple shortcuts to the same customer report, and simply specify different projects in the sort criteria for the projects you need to report in.
Thank you,
Tom Harder
Axosoft Support
support@axosoft.com1.800.653.0024 option 3--Axosoft University--